Overview: Breast cancer is the second most prevalent cancer in New Zealand with a largely unclear genetic etiology. Recent progress has demonstrated that expression of tumour suppressor proteins is regulated by long non-coding RNA. At chromosome position 9p21 the tumour suppressor p16INK4A and the long non-coding RNA antisense non-coding RNA in the INK4 locus (ANRIL) are both encoded. Inherited variants in p16INK4A including the minor allele of the rs11515 (C/G500) polymorphism at the 3’UTR region are more frequent in breast cancer patients. The rs11515 allele was associated with increased ANRIL and reduced p16INK4A expression. This study aimed to develop a method to type the rs11515 alleles in formalin fixed tissue for use when only archival material is made available. The study also aimed to confirm the previous association between ANRIL and p16INK4A and identify the cell type responsible for increased ANRIL in breast cancer tissues. Lastly the study aimed to investigate ANRIL expression in a wide range of tissues to obtain a better understanding of where ANRIL is expressed.

Hypothesis: The rs11515 CG genotype is associated with higher ANRIL in malignant breast cancer cells. Expression of ANRIL will vary between tissues and a better understanding of ANRIL expression in multiple tissues will identify future tissue types to investigate the effect of rs11515 genotypes

Conclusion: Increased ANRIL and p16INK4A were found in rs11515 heterozygotes whereas the presence of ER/PR status influenced the co-expression in both genotypes. The increased ANRIL with the CG genotype was consistent with that found earlier; however, the positive correlation between ANRIL and p16INK4A differed from the inverse correlation found previously. In Situ Hybridisation showed ANRIL in malignant cells. The multiple tissue based analysis suggested a tissue specific co-expression profiles for ANRIL and p16INK4A